scholarly journals An Alternative Splice Variant of HIPK2 with Intron Retention Contributes to Cytokinesis

Cells ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 484 ◽  
Author(s):  
Veronica Gatti ◽  
Manuela Ferrara ◽  
Ilaria Virdia ◽  
Silvia Matteoni ◽  
Laura Monteonofrio ◽  
...  

HIPK2 is a DYRK-like kinase involved in cellular stress response pathways, development, and cell division. Two alternative splice variants of HIPK2, HIPK2-FL and HIPK2-Δe8, have been previously identified as having different protein stability but similar functional activity in the stress response. Here, we describe one additional HIPK2 splice variant with a distinct subcellular distribution and functional activity in cytokinesis. This novel splice variant lacks the last two exons and retains intron13 with a stop codon after 89 bp of the intron, generating a short isoform, HIPK2-S, that is detectable by 2D Western blots. RT-PCR analyses of tissue arrays and tumor samples show that HIPK2-FL and HIPK2-S are expressed in normal human tissues in a tissue-dependent manner and differentially expressed in human colorectal and pancreatic cancers. Gain- and loss-of-function experiments showed that in contrast to HIPK2-FL, HIPK2-S has a diffuse, non-speckled distribution and is not involved in the DNA damage response. Rather, we found that HIPK2-S, but not HIPK2-FL, localizes at the intercellular bridge, where it phosphorylates histone H2B and spastin, both required for faithful cell division. Altogether, these data show that distinct human HIPK2 splice variants are involved in distinct HIPK2-regulated functions like stress response and cytokinesis.

Botany ◽  
2013 ◽  
Vol 91 (12) ◽  
pp. 840-849 ◽  
Author(s):  
Joshua Powles ◽  
Katharine Sedivy-Haley ◽  
Eric Chapman ◽  
Kenton Ko

Rhomboid serine proteases are grouped into three main types — secretases, presenilin-like associated rhomboid-like (PARL) proteases, and “inactive” rhomboid proteins. Although the three rhomboid groups are distinct, the different types are likely to operate within the same cell or compartment, such as observed in the plastids of Arabidopsis. There are four distinct plastid rhomboid genes at play in Arabidopsis plastids, two for active types (At1g25290 and At5g25752) and two for inactive forms (At1g74130 and At1g74140). The number of working plastid rhomboids is further increased by alternative splicing, as reported for At1g25290. To understand how the plastid rhomboid system works, it is necessary to identify all rhomboid forms in play. To this end, this study was designed to examine the alternative splicing activities of At1g74130, one of the two genes encoding proteolytically “inactive” plastid rhomboids. The exon mapping and DNA sequencing results obtained here indicate the presence of three prominent alternative splice variants in the At1g74130 transcript population. The dominant splice variant, L, encodes the full-length protein. The other two splice variants, M and S, produce proteins lacking sections from the carboxyl transmembrane domain region. The splice variants M and S appear to be at levels with functional potential and appear to adjust relative to each other during development and in response to changes in the level of Tic40, a component of the plastid translocon. The splice variant proteins themselves exhibit different characteristics with respect to rhomboid protein–substrate interactions. These differences were observed in bacterial co-expression pull-down assays and in yeast mitochondrial studies. When considered together, the data suggest that the alternative splicing of At1g74130 bears functional significance in Arabidopsis and is likely to be part of a mechanism for diversifying plastid rhomboid function.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 35-35
Author(s):  
Sara L. Seegers ◽  
Amanda Lance ◽  
Lawrence J Druhan ◽  
Belinda R Avalos

CSF3R, the receptors for granulocyte colony stimulating factor, is a critical regulator of neutrophil production. Multiple CSF3R mRNA transcripts have been identified and are annotated in Genbank. The expression and function of the different CSF3R proteins have not been fully elucidated. We generated antibodies specific for two of the identified and annotated isoforms, V3 and V4. CSF3R-V4 is a truncated variant of V1 with a unique C-terminal 34 amino acids and this variant confers enhanced growth signals. Changes in the ratio of V1:V4 isoforms have been implicated in chemotherapy resistance and relapse of AML. CSF3R-V3 is a variant of V1 with a 27 amino acid insertion between two conserved domains in the cytoplasmic portion of the receptor involved in JAK/STAT activation, termed the box 1 and box 2. CSF3R-V3 produces reduced proliferative signaling in response to G-CSF. When V3 is co-expressed with V1, proliferative signaling is reduced in a concentration dependent manner. In order to generate custom rabbit polyclonal antibodies specific for CSF3R-V3 and CSF3R-V4 we used either a peptide that corresponds to a unique amino acid sequence present only in CSF3R-V3 or a peptide specific for a portion of the C-terminal amino acid sequence unique to the CSF3R-V4 isoform conjugated to an immunogenic carrier protein. These immunogens both produced robust immune responses, and the polyclonal antibodies were subsequently purified from bulk sera. Immunoblot analysis of lysates from Ba/F3 cells expressing CSF3R-V1 (V1), CSF3R-V3 (V3), or CSF3R-V4 (V4) demonstrated that both the custom generated anti-CSF3R-V3 and anti-CSF3R-V4 antibodies were very specific, recognizing only the appropriate CSF3R receptor isoform. All three CSF3R splice variants are recognized by commercially available anti-CSF3R (clone LMM741 to CD114), while the anti-CSF3R-V4 custom antibody and the custom anti-CSF3R-V3 antibody recognizes only the CSF3R-V4 and CSF3R-V3 isoforms, respectively. We next sought to detect the CSF3R receptor isoforms in primary human cells. Using our custom antibodies, we detected for the first time, both the CSF3R-V3 and CSF3R-V4 receptor forms in primary neutrophils isolated from healthy donors. Each of the CSF3R isoforms produce unique signaling, and we hypothesized that the observed differences in G-CSF-dependent signaling is produced by the expression level of each receptor isoform via both homodimerization and by heterodimerization of the receptor splice variant proteins. To investigate the potential for heterodimerization of the CSF3R-V1 with the V3 and V4 isoforms, we generated a CSF3R-V1 with a c-terminal epitope tag and co-expressed this construct with both CSF3R-V3 or CSF3R-V4. Immunoprecipitation with an antibody to the epitope tag (recognizing the V1 variant) followed by immunoblotting with the custom anti-V3 or anti-V4 antibodies demonstrated that both CSF3R-V3 and CSF3R-V4 co-immunoprecipitated with CSF3R-V1, in agreement with our hypothesis that the splice variants form receptor heterodimers. Of note, the CSF3R receptor heterodimers are detected even in the absence of G-CSF, thus demonstrating that CSF3R exist as a preformed receptor dimer in an inactive state. In conclusion, we have generated antibodies that specifically detect the CSF3R-V3 and the CSF3R-V4 receptor proteins. These are the first studies to demonstrate the expression of the CSF3R splice variants at the protein level, in both cell lines and primary human cells. In addition, these are the first studies to demonstrate the formation of heterodimers of the CSF3R splice variants, providing a mechanism for the observed alteration in ligand-dependent signaling produced under conditions of altered splice variant expression. Disclosures Avalos: Juno: Membership on an entity's Board of Directors or advisory committees; Best Practice-Br Med J: Patents & Royalties: receives royalties from a coauthored article on evaluation of neutropenia.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2630-2630
Author(s):  
Nels Olson ◽  
Bruce Scott ◽  
George Long ◽  
Edwin Bovill

Abstract Introduction: A genome-wide scan of linkage with venous thrombosis in a thrombophilic kindred with type I protein C deficiency identified a candidate region on chromosome 11q23 (P<0.0001). Located at the linkage peak is PAFAH1B2, the β-subunit of the intracellular form of PAFAH. Intracellular PAFAH is a heterodimer of alpha and beta subunits both of which have catalytic activity. PAFAH reduces intracellular PAF levels and a reduction in active PAFAH likely leads to an enhanced inflammatory response at the vascular wall. Resequencing experiments revealed a novel splice variant for the intracellular form of PAFAH. The current study characterizes this novel splice variant that results in the deletion of exon 6 and its catalytic domain and the introduction of an alternative 7th exon. Methods: Identification of novel mRNA splice variants was achieved by sequencing PCR products obtained from amplifying known regions of PAFAH 1B2 mRNA. Confirmation of the exon 5 to 7 splice and exon 7 polyadenylation were obtained from sequencing 3′RACE products. Protein extracts were resolved by SDS- PAGE and Western blotted. Results: An alternative splice form of PAFAH 1B2 was isolated and sequenced. This isoform was observed in cDNA from human liver, moncytes, and T and B lymphocytes using PCR. This variant contains the first five exons of the native form protein and replaces exon 6 with an alternative 7th exon located downstream of exon 6. Exon 6 contains two residues involved in the protein’s active site triad, Asp and His, and are absent in exon 7. Computer modeling suggests replacement of exon 6 by exon 7 would abolish the active site and possibly alter the proteins’ ability to dimerize. Preliminary Western blots from selected tissues demonstrated the presence in liver of a new band consistent with the predicted size of the variant. Conclusions: We hypothesize that this alternative splice likely decreases the proteins ability to function as a regulator of inflammation. We are presently carrying out gene expression analysis to determine the relative levels of the splice variant in different tissues and changes in expression associated with activation of leukocytes.


2015 ◽  
Vol 36 (5) ◽  
pp. 693-713 ◽  
Author(s):  
Christopher J. Huggins ◽  
Manasi K. Mayekar ◽  
Nancy Martin ◽  
Karen L. Saylor ◽  
Mesfin Gonit ◽  
...  

The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances, and endoplasmic reticulum (ER) stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its recruitment tocis-regulatory C/EBP:ATF response elements (CAREs) together with a dimeric partner of uncertain identity. Here, we show that C/EBPγ:ATF4 heterodimers, but not C/EBPβ:ATF4 dimers, are the predominant CARE-binding species in stressed cells. C/EBPγ and ATF4 associate with genomic CAREs in a mutually dependent manner and coregulate many ISR genes. In contrast, the C/EBP family members C/EBPβ and C/EBP homologous protein (CHOP) were largely dispensable for induction of stress genes.Cebpg−/−mouse embryonic fibroblasts (MEFs) proliferate poorly and exhibit oxidative stress due to reduced glutathione levels and impaired expression of several glutathione biosynthesis pathway genes.Cebpg−/−mice (C57BL/6 background) display reduced body size and microphthalmia, similar to ATF4-null animals. In addition, C/EBPγ-deficient newborns die from atelectasis and respiratory failure, which can be mitigated byin uteroexposure to the antioxidant,N-acetyl-cysteine.Cebpg−/−mice on a mixed strain background showed improved viability but, upon aging, developed significantly fewer malignant solid tumors than WT animals. Our findings identify C/EBPγ as a novel antioxidant regulator and an obligatory ATF4 partner that controls redox homeostasis in normal and cancerous cells.


2017 ◽  
Author(s):  
Wenfa Ng

Structure informs function, and this may be the evolutionary reason why alternative splicing, which is capable of generating different variants of the same protein, arise. But, given the energetic cost of generating different splice variants for testing their capability at a specific task, which incurs cellular functional uncertainty; as well as the exertion of differing physiological effects on cells that may translate into diseased states, what is the evolutionary advantage of this process? Additionally, what are the factors that select a specific variant for a presented task? Using heart tissue samples exposed to hypoxia stress as model system, this research idea entails the illumination of single nucleotide polymorphisms (SNP) of the calcium channel transporter, Cav 1.2 gene in the population through gene sequencing followed by bioinformatic analysis for alternative splice sites. This would be followed by a scan for alternative splice variants through colony polymerase chain reaction using universal primers for Cav 1.2 gene. Confirmation of splice variant identity through Western blot laid the stage for subsequent efforts at cloning and expressing the variant gene in HEK 293 cells lacking endogenous expression of Cav 1.2, for biophysical characterization of calcium conduction through patch clamp electrophysiology. In parallel, structural elucidation efforts necessitate the purification of the calcium channel via hydrophobic interaction or reversed phase liquid chromatography after its heterologous expression in a bacterial host. But, biophysical and biochemical characterization does not speak of the signaling and metabolic pathways laying the path to generation of the splice variant(s). Hence, discovery approaches such as RNA-seq and mass spectrometry proteomics could uncover the molecular mysteries at the transcript and protein level that help guide the selection of specific splice variant in response to hypoxic stress, where HIF is a candidate pathway. Implementing this approach from the retrospective angle of examining diseased human tissue samples provide one important facet for uncovering possible mechanisms driving the generation of a splice variant. However, the complementary prospective approach of identifying the molecular basis and processes for responding to hypoxia in a cell line such as HEK 293 would help provide confirmatory evidence in understanding the key drivers of physiological response to lack of oxygen at the cellular level. Collectively, this research route would illuminate both the nucleotide informational basis of alternative splicing in calcium channel Cav 1.2 as well as identify the molecular mechanisms enabling the selection of specific splice variants useful for conferring, at the cell and tissue level, ability to withstand hypoxic stress without significant negative effects on cell function. Interested readers can expand on the ideas presented.


2006 ◽  
Vol 290 (1) ◽  
pp. F117-F126 ◽  
Author(s):  
Wei Tian ◽  
Yi Fu ◽  
Donna H. Wang ◽  
David M. Cohen

The capsaicin receptor and transient receptor potential channel TRPV1 senses heat, protons, and vanilloid agonists in peripheral sensory ganglia. Abundant data have suggested the presence of potentially novel splice variants in the kidney. We report a novel rat TRPV1 splice variant, TRPV1VAR, cloned from kidney papilla. TRPV1VAR cDNA was identified in multiple kidney tissues. Its sequence was fully compatible with potential splice donor and acceptor sites in the rat TRPV1 gene. TRPV1VAR is predicted to encode a truncated form of TRPV1 consisting of the NH2-terminal 248 residues of TRPV1 (all within the NH2-terminal intracellular domain) followed by five nonconsensus amino acids (Arg-Glu-Ala-Met-Trp) and a stop codon. The variant utilizes the same consensus Kozak sequence as canonical TRPV1. A band of the appropriate molecular mass was identified in rat kidney papillary (but not medullary) lysates immunoblotted with an antibody directed against the NH2 terminus of TRPV1, whereas an antibody recognizing the TRPV1 COOH terminus failed to detect it. Upon heterologous expression in HEK 293 cells, TRPV1VAR potentiated the ability of cotransfected TRPV1 to confer calcium influx in response to resiniferatoxin. TRPV1VAR did not influence expression or cell surface localization of cotransfected TRPV1. TRPV1VAR protein product associated with the NH2 terminus of canonical TRPV1. Interestingly, when expressed in the COS-7 epithelial cell line, TRPV1VAR functioned in a dominant-negative acting capacity, partially blocking TRPV1-dependent resiniferatoxin responsiveness. We conclude that TRPV1VAR is one of perhaps several TRPV1 splice variants expressed in rat kidney and that it may serve to modulate TRPV1 responsiveness in some tissues.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 3130-3130
Author(s):  
Amanda Lance ◽  
Rajeswaran Mani ◽  
Sara L. Seegers ◽  
Belinda R Avalos ◽  
Lawrence J Druhan

Abstract The granulocyte colony stimulating factor receptor (CSF3R) is a critical regulator of neutrophil production with multiple alternatively spliced variants. The truncated CSF3R-V4 splice variant confers enhanced growth signals, and changes in its expression levels relative to the canonical V1 (wild type) isoform have been implicated in chemotherapy resistance and relapse of AML. We previously demonstrated that the CSF3R-V3 isoform, a variant of V1 with an insertion in the cytoplasmic domain, produces hypoproliferative signals in lymphoid cells in response to G-CSF. We also reported that expression of all three splice variants is significantly altered in AML, suggesting that aberrant CSF3R splicing is involved in the pathogenesis of some myeloid malignancies. The functional signaling capabilities of the different CSF3R isoforms in regulating granulopoiesis remain largely unknown. Herein, we describe a novel myeloid model system and show that the V3 and V4 isoforms generate opposing proliferative signals without effects on myeloid cell differentiation. ER-HoxB8 cells are murine bone marrow progenitor cells ectopically expressing an ER-HoxB8 fusion protein, and in the presence of estradiol (E2) the fusion protein dimerizes producing a functional HoxB8 dimer which enforces self-renewal. Thus, in the presence of E2 these cells continually proliferate; however, when E2 is withdrawn they differentiate into mature granulocytes. Addition of G-CSF to culture medium of E2 ER-HoxB8 cells increases progenitor cell proliferation in a dose dependent manner (Figure 1A). Using CRISPR/Cas9, we knocked-out the endogenous murine Csf3r. As expected, ER-HoxB8-Csf3r-/- cells still produced mature neutrophils with E2 withdrawal and no increase in differentiation or proliferation of the knock-out cells (KO) was observed in response to G-CSF. The functional behavior of our ER-HoxB8-Csf3r-/- cells recapitulates the published phenotype of the Csf3r knock-out mouse, which exhibits severe neutropenia but has circulating neutrophils. ER-HoxB8 KO cells were transduced with human CSF3R splice variants and expression confirmed by immunoblot analysis using splice-variant specific antibodies. KO cells expressing the CSF3R-V3 demonstrated a hypoproliferative response to G-CSF with an ~40-fold increase in the EC50 relative to cells expressing CSF3R-V1 (Figure 1B), confirming our prior observations in the lymphoid BaF3 cell line. In contrast, KO cells expressing the truncated CSF3R-V4 variant hyperproliferated in response to G-CSF consistent with our previously published data in lymphoid cells. Using multi-color flow cytometry with antibodies against CD117, CD11b, and Ly6G to identify progenitor, intermediately differentiated cells (NeuP), and mature neutrophils, we found that KO cells (like parental ER-HoxB8 cells) produced significant numbers of CD11b+/LyGG- NeuP cells upon E2 withdrawal and addition of G-CSF had no effect on differentiation. Transduction of ER-HoxB8 KO cells with the wild type human CSF3R-V1 restored their capacity to respond to G-CSF in a dose dependent manner. KO cells transduced with CSF3R-V3 displayed normal production of NeuP cells with E2 withdrawal, and addition of G-CSF produced a substantial increase in the numbers of mature neutrophils (CD11b+, Ly6G+) after 5 days in culture, relative to KO cells (Figure 2C). Thus, we have demonstrated that CSF3R-V3 is able to support the production of fully mature neutrophils. Notably, a G-CSF induced increase in the numbers of mature neutrophils was also evident in CSF3R-V4 transduced cells. Previous work by others indicated that CSF3R-V4 was not able to drive myeloid differentiation. We hypothesize that this difference in phenotype is due to a V4-dependent hyperproliferation of the neutrophil progenitors. On-going work is focused on the determination of the specific effects these CSF3R splice variants have on each stage of granulopoiesis. In conclusion, using our novel engineered CSF3R model system, we confirm differential effects of CSF3R splice variants on myeloid cell proliferation and show sustained differentiation capacity of each isoform. Additional studies using this model system provide the opportunity for identification of new therapeutic targets for treatment of disorders of granulocyte production. Figure 1 Figure 1. Disclosures Avalos: JUNO: Membership on an entity's Board of Directors or advisory committees.


2015 ◽  
Vol 465 (3) ◽  
pp. 489-501 ◽  
Author(s):  
Moshe Giladi ◽  
Su Youn Lee ◽  
Reuben Hiller ◽  
Ka Young Chung ◽  
Daniel Khananshvili

Ca2+ binding to CBD1 (calcium-binding domain 1) and CBD2 regulates Na+/Ca2+ exchangers (NCX). In the present study, we demonstrate that Ca2+ binding rigidifies the main chain of CBD2, but not of CBD1, in a splice variant-dependent manner. The dynamic differences account for variant-dependent responses to Ca2+.


2012 ◽  
Vol 30 (27_suppl) ◽  
pp. 35-35 ◽  
Author(s):  
Salma Khan ◽  
Yuan Yuan ◽  
Malyn May Valenzuela ◽  
David Turay ◽  
Heather Ferguson ◽  
...  

35 Background: The inhibitor of apoptosis (IAP) protein Survivin and its splice variants are differentially expressed in breast cancer tissues and have recently been shown to be released from tumor cells via small membrane-bound vesicles called exosomes. Tumor-derived exosomes play multiple roles in tumor growth and metastasis and may produce these functions by impacting immune escape, tumor invasion and angiogenesis. We, therefore, hypothesize that analysis of exosomal Survivin and its splice variants may provide a novel biomarker for early diagnosis of breast cancer in addition to current recommended methods. Methods: Twenty paired breast cancer patient’s sera and tumor tissue, and ten normal control sera were used for analysis. ELISA was performed to quantitate serum levels of Survivin. Exosomes were isolated from the sera using Exoquick. RT-PCR, western blots with densitometry, and immunohistochemistry followed by confocal microscopy were then performed. Results: For each breast cancer patient serum, Survivin levels were significantly higher compared to control (p<0.05). While Survivin and the DEx3 splice variant expression and localization were similar, differential expression of Survivin and the 2B splice variant protein and mRNA existed in the exosomes and tissue samples. Survivin and -DEx3 proteins were the predominant forms detected in 100% (20/20) of the breast cancer tissues evaluated, whereas a more variable expression of Survivin-2B, with enhanced levels found in areas of necrosis. We also for the first time here show the exosomal localization of Survivin and its splice variants DEx3 and 2B in sera from breast cancer patients. Conclusions: The result of the proposed project supports our hypothesis that differential expression of exosomal-Survivin and its alternative splice variants may serve as a diagnostic marker in breast cancer patients. For future direction, we plan to study the prognostic value of exosomal-Survivin and its splice variants on a large panel of primary breast cancers within a setting of well-followed clinical outcomes.


2017 ◽  
Author(s):  
Wenfa Ng

Structure informs function, and this may be the evolutionary reason why alternative splicing, which is capable of generating different variants of the same protein, arise. But, given the energetic cost of generating different splice variants for testing their capability at a specific task, which incurs cellular functional uncertainty; as well as the exertion of differing physiological effects on cells that may translate into diseased states, what is the evolutionary advantage of this process? Additionally, what are the factors that select a specific variant for a presented task? Using heart tissue samples exposed to hypoxia stress as model system, this research idea entails the illumination of single nucleotide polymorphisms (SNP) of the calcium channel transporter, Cav 1.2 gene in the population through gene sequencing followed by bioinformatic analysis for alternative splice sites. This would be followed by a scan for alternative splice variants through colony polymerase chain reaction using universal primers for Cav 1.2 gene. Confirmation of splice variant identity through Western blot laid the stage for subsequent efforts at cloning and expressing the variant gene in HEK 293 cells lacking endogenous expression of Cav 1.2, for biophysical characterization of calcium conduction through patch clamp electrophysiology. In parallel, structural elucidation efforts necessitate the purification of the calcium channel via hydrophobic interaction or reversed phase liquid chromatography after its heterologous expression in a bacterial host. But, biophysical and biochemical characterization does not speak of the signaling and metabolic pathways laying the path to generation of the splice variant(s). Hence, discovery approaches such as RNA-seq and mass spectrometry proteomics could uncover the molecular mysteries at the transcript and protein level that help guide the selection of specific splice variant in response to hypoxic stress, where HIF is a candidate pathway. Implementing this approach from the retrospective angle of examining diseased human tissue samples provide one important facet for uncovering possible mechanisms driving the generation of a splice variant. However, the complementary prospective approach of identifying the molecular basis and processes for responding to hypoxia in a cell line such as HEK 293 would help provide confirmatory evidence in understanding the key drivers of physiological response to lack of oxygen at the cellular level. Collectively, this research route would illuminate both the nucleotide informational basis of alternative splicing in calcium channel Cav 1.2 as well as identify the molecular mechanisms enabling the selection of specific splice variants useful for conferring, at the cell and tissue level, ability to withstand hypoxic stress without significant negative effects on cell function. Interested readers can expand on the ideas presented.


Sign in / Sign up

Export Citation Format

Share Document